Contacts of the helix formed by residues 46 - 55 (chain B) in PDB entry 6CNC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ILE* 5.1 6.7 - - + -
42B GLN* 5.5 1.1 - - + -
43B ASP* 2.9 33.0 + - + +
45B TRP* 1.3 104.0 - + + +
47B LEU* 1.3 62.2 + - - +
48B LEU 3.5 0.2 - - - -
49B PRO* 3.9 7.8 - - - +
50B ALA* 4.2 6.8 + - - +
627B LEU* 5.2 2.9 - - + -
630B LEU* 3.9 15.9 - - + +
631B LEU* 3.7 37.0 - - + +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ASP 4.2 0.2 + - - -
44B LYS* 3.0 20.9 + - - +
45B TRP 3.0 0.6 + - - -
46B HIS* 1.3 77.5 - - - +
48B LEU* 1.3 68.0 + - - +
50B ALA* 3.2 7.3 + - - +
51B PHE* 2.9 22.3 + - + +
613B ILE* 3.7 20.9 - - + -
622B VAL* 5.7 2.9 - - + -
627B LEU* 3.7 24.0 - - + -
630B LEU* 4.1 5.2 - - + -
637B PHE* 5.6 4.8 - - + -
640B PHE* 3.4 34.1 - - + -
646B VAL* 5.4 3.4 - - + -
675B ILE* 3.7 37.7 - - + -
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TRP* 3.3 2.2 + - - +
47B LEU* 1.3 79.5 - - - +
49B PRO* 1.3 58.9 - - + +
51B PHE* 3.1 10.1 + - + +
52B LEU* 2.6 49.2 + - + -
516B LEU* 5.1 6.5 - - + -
517B MET* 3.5 39.5 - - + -
675B ILE* 4.6 5.6 - - + -
676B GLU* 3.1 35.6 + - - +
678B PHE* 5.2 3.4 - - + -
679B THR* 4.3 11.2 - - - +
743B LEU* 3.4 31.0 - - + -
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Residues in contact with PRO 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TRP* 3.4 46.2 - - + +
46B HIS* 3.9 6.1 - - - +
47B LEU 3.6 2.0 - - - -
48B LEU* 1.3 92.3 - - + +
50B ALA* 1.3 51.9 + - - +
52B LEU* 2.9 6.0 + - + +
53B LYS* 2.4 42.0 + - + +
743B LEU* 4.3 17.5 - - + -
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B HIS 4.2 9.0 + - - +
47B LEU 3.2 9.2 + - - +
49B PRO* 1.3 77.9 - - - +
51B PHE* 1.3 63.3 + - - +
53B LYS* 4.1 9.4 - - + -
54B VAL* 3.1 31.0 + - + +
630B LEU* 4.6 21.8 - - + -
636B ASP* 4.9 11.9 - - + -
637B PHE* 4.4 2.9 - - + -
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 2.9 13.3 + - + +
48B LEU* 3.1 15.0 - - + +
50B ALA* 1.3 77.1 - - - +
52B LEU* 1.3 67.5 + - + +
54B VAL* 4.2 1.0 - - - +
55B LYS* 3.2 65.2 + - - +
516B LEU 4.9 3.1 - - - -
517B MET* 3.6 48.7 - - + -
518B THR 5.4 2.0 - - - -
519B HIS* 5.5 2.2 - - + -
611B PRO* 3.7 19.3 - - + -
637B PHE* 3.2 54.0 - + + +
648B TYR* 4.4 2.9 - + - -
675B ILE* 6.0 0.4 - - + -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 2.6 38.5 + - + +
49B PRO* 3.8 4.5 - - + +
51B PHE* 1.3 78.5 - - + +
53B LYS* 1.3 63.2 + - - +
55B LYS 2.9 23.4 - - - +
56B GLY* 3.7 4.9 - - - -
57B LEU* 4.4 37.0 - - + +
516B LEU* 4.5 20.4 - - + +
743B LEU* 4.1 32.5 - - + +
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PRO* 2.4 32.3 + - + +
50B ALA* 3.8 8.3 - - + +
52B LEU* 1.3 70.9 - - - +
54B VAL* 1.3 71.2 + - + +
55B LYS 4.7 0.3 - - - -
56B GLY* 4.9 1.6 + - - -
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA* 3.1 17.5 + - - +
51B PHE 4.2 1.6 - - - +
53B LYS* 1.3 84.2 - - + +
55B LYS* 1.3 64.7 + - + +
56B GLY 3.5 2.6 + - - -
636B ASP* 4.3 26.5 - - + +
637B PHE* 4.5 19.5 - - + +
638B ASP* 5.0 9.0 - - - +
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B PHE* 3.2 56.9 + - + +
52B LEU* 2.9 16.2 - - - +
54B VAL* 1.3 81.6 - - + +
56B GLY* 1.3 72.1 + - - +
59B LYS* 3.4 36.8 - - + +
60B GLN* 5.9 0.4 - - - +
63B ASP* 4.8 4.0 - - - +
518B THR 4.5 4.4 + - - -
519B HIS* 3.4 31.6 - - + +
637B PHE* 5.3 4.0 - - + -
638B ASP* 5.9 7.0 - - - +
648B TYR* 4.2 4.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il